Guppy in a Singularity Container - JoshLoecker/MAPT GitHub Wiki

Guppy currently exists in a Singularity container for its ease of use, reproducibility, and separation from SciNet's own packages.
If you would like to use any of Guppy's software (basecalling, barcoding, etc.), simply perform the following

1. Locate the Guppy container (this is most likely found at /project/brookings_minion/guppy_container.sif)
2. Execute singularity exec /proejct/brookings_minion/guppy_container.sif COMMAND
   a. COMMAND is the command you would like to execute inside the container

Examples

Input: singularity exec /proejct/brookings_minion/guppy_container.sif guppy_basecaller --version
Output: : Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 4.2.2+effbaf84

Input: singularity exec /proejct/brookings_minion/guppy_container.sif guppy_barcoder --version
Output: guppy_barcoder, part of Guppy basecalling suite, (C) Oxford Nanopore Technologies, Limited. Version 4.2.2+effbaf84

Input: singularity exec /proejct/brookings_minion/guppy_container.sif guppy_basecaller --config "dna_r9.4.1_450bps_hac.cfg" --input_path /project/brookings_minion/fast5_input --save_path /project/brookings_minion/fast5_output Output: The processing of fast5 files directly under the input_path directory

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